CDS Annotation in Full-Length cDNA Sequence
Open Access
- 2 June 2003
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 13 (6b), 1478-1487
- https://doi.org/10.1101/gr.1060303
Abstract
The identification of coding sequences (CDS) is an important step in the functional annotation of genes. CDS prediction for mammalian genes from genomic sequence is complicated by the vast abundance of intergenic sequence in the genome, and provides little information about how different parts of potential CDS regions are expressed. In contrast, mammalian gene CDS prediction from cDNA sequence offers obvious advantages, yet encounters a different set of complexities when performed on high-throughput cDNA (HTC) sequences, such as the set of 60,770 cDNAs isolated from full-length enriched libraries of the FANTOM2 project. We developed a CDS annotation strategy that uses a variety of different CDS prediction programs to annotate the CDS regions of FANTOM2 cDNAs. These include rsCDS, which uses sequence similarity to known proteins; ProCrest; Longest-ORF and Truncated-ORF, which are ab initio based predictors; and finally, DECODER and NCBI CDS predictor, which use a combination of both principles. Aided by graphical displays of these CDS prediction results in the context of other sequence similarity results for each cDNA, FANTOM2 CDS inspection by curators and follow-up quality control procedures resulted in high quality CDS predictions for a total of 14,345 FANTOM2 clones.Keywords
This publication has 12 references indexed in Scilit:
- Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA CollectionGenome Research, 2003
- The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular EnvironmentGenome Research, 2003
- Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation SystemGenome Research, 2003
- Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAsNature, 2002
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- Identification of MAL2, a Novel Member of the MAL Proteolipid Family, Though Interactions with TPD52-like Proteins in the Yeast Two-Hybrid SystemGenomics, 2001
- Amino acid translation program for full-length cDNA sequences with frameshift errors.Physiological Genomics, 2001
- A Perfect Message: RNA Surveillance and Nonsense-Mediated DecayCell, 1999
- Binary specification of nonsense codons by splicing and cytoplasmic translationThe EMBO Journal, 1998
- Recognition of UGA as a selenocysteine codon in Type I deiodinase requires sequences in the 3′ untranslated regionNature, 1991